1,720,959 research outputs found
Resecuenciación de genomas de sorgo (Sorghum bicolor L.): Polimorfismos y su impacto funcional en la acumulación de azúcares y producción de biomasa
No full textCientos de mapeos de loci de caracteres cuantitativos (QTL) han sido realizados en sorgo (Sorghum bicolor L.) con muy pocos genes causales identificados y validados. Este trabajo parte de un mapeo de QTL de alta resolución en una población de líneas recombinantes endocriadas (RILs) obtenidas cruzando un sorgo granífero (M71) con uno dulce (SS79), en el que se identificaron 38 QTLs asociados a la acumulación de azúcar y producción de biomasa y un total de 3.174 genes candidatos (GC) posicionales. A fin de identificar polimorfismos entre los genomas parentales de la población, se realizó una resecuenciación en un Illumina Novaseq 6000 (celda de flujo S4, 300 ciclos, PE150). Usando BTx623 v3.1 como genoma de referencia se identificaron SNPs e InDels utilizando SNiPPY3.1, detectándose un total de 109.579 polimorfismos entre M71 y SS79 en los 38 QTLs. El impacto funcional de los polimorfismos sobre la función de los alelos parentales en los GC posicionales se evaluó utilizando SNPeff (151 GC con impacto alto, 754 moderado, 2.418 modificante y 701 bajo). De especial interés resultan aquellos alelos portadores de polimorfismos con impacto funcional alto que puedan explicar parte del contraste fenotípico observado entre los parentales. Por ejemplo, el gen ma1 en M71 presenta una deleción en el exón 1 que modifica el marco de lectura y trunca la proteína codificada. Este reconocido inhibidor de la floración colocaliza con un QTL de altura y producción de biomasa. Un análisis detallado de polimorfismos/ impactos nos permitió priorizar una lista de GC para futuras evaluaciones funcionales.Fil: Carrere Gómez, Manuela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires; ArgentinaFil: Chakrabarty, Subhadra. Justus Liebig Universitat Giessen; AlemaniaFil: Baricalla, Agustin Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Centro de Bioinvestigaciones (Sede Pergamino); ArgentinaFil: Snowdon, Rod. Justus Liebig Universitat Giessen; AlemaniaFil: Federico, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria Pergamino; ArgentinaL Congreso Argentino de Genética; II Jornadas Regionales SAG-NEACorrientesArgentinaSociedad Argentina de GenéticaUniversidad Nacional del Nordeste. Facultad de Ciencias Exactas y Naturales y Agrimensur
Prioritization of candidate genes in QTL regions associated with bioenergy-related traits in sorghum (Sorghum bicolor) using a machine learning algorithm
No full textGene prioritization pipelines are designed to rank positional candidate genes (CG) within quantitative trait loci (QTL) and reduce the list of CG that is selected for further in-depth functional analysis. We have designed an integrated approach to prioritize CG in sorghum (Sorghum bicolor) combining the use of high-resolution QTL mapping, a machine learning algorithm, sequence analysis of the parental genomes and CG expression profiling. First, we re-mapped QTL associated with 20 different bioenergy-related traits in a recombinant inbred line (RIL) population from a cross between grain (M71) and sweet sorghum (SS79), genotyped using an Affymetrix 90K sorghum single nucleotide polymorphism (SNP) array. Thirty-eight QTL for 16 traits were identified using composite interval mapping; reference genome coordinates were determined for each QTL confidence interval and lists of positional CG generated. Positional CG lists were ranked using a machine learning algorithm, QTG-Finder2. Genomes of the RIL parental lines were re-sequenced in an Illumina NovaSeq 6000 (S4 flow cell, 300 cycles, PE150). Sequencing reads were aligned to the sorghum reference genome, BTx623, and SNPs were called for the parental genotypes. SNP effects on parental allele function were assessed using SNPeff. We also evaluated the tissue-specificity of each of the top 20% CG ranked by QTG-Finder2. Lastly, we generated a prioritized list of positional CG for each of the 38 QTL based on QTG-Finder2 rank, SNP presence/effect between parental alleles and expression profile. Taken together, these results bring us a step closer to finding the causal genes behind these set of bioenergy-associated traits.Fil: Federico, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria Pergamino; ArgentinaFil: Carrere Gómez, Manuela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria Pergamino; ArgentinaFil: Chakrabarty, Subhadra. Justus Liebig Universitat Giessen; AlemaniaFil: Erazzú, Luis Ernesto. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Tucuman-Santiago del Estero. Estación Experimental Agropecuaria Famaillá; ArgentinaFil: Snowdon, Rod. Justus Liebig Universitat Giessen; AlemaniaXVIII Latin American Congress of Genetics; LIV Annual Meeting of the Chilean Society of Genetics; XLIX Argentine Congress of Genetics; VIII Congress of the Uruguayan Society of Genetics; I Paraguayan Congress of Genetics; V Latin American Congress of Human GeneticsValdiviaChileSociedad Argentina de GenéticaSociedad de Genética de ChileSociedad Uruguaya de GenéticaAsociación Latinoamericana de GenéticaSociedad Paraguaya de GenéticaRed Latinoamericana de Genética Human
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Genetic dissection of cold tolerance in sorghum (Sorghum bicolor L. Moench)
Full text linkSorghum (Sorghum bicolor L. Moench), the 5th most important cereal crop belongs to the Poaceae grass family. According to records, it originated around 7000-5000 BC in the north-eastern part of Africa from where it traveled across the different parts of Africa, the middle east, India, China and eventually Americas, Australia, and finally Europe. As a result of multiple complex genomic interactions and selection, pressure can be broadly subdivided into the botanical classification of S. halepense, S. propinquum, and S. bicolor, and classification of cultivated forms of S. bicolor subsp. bicolor into five races, namely bicolor, guinea, caudatum, kafir, and durra. It is mainly grown in the lowlands and semi-arid regions of the tropics and subtropics and has been adapted to various contrasting environments for different end-products leading to an increase in morphological and genetic diversity. For example, in African countries, it is primarily grown as food grain and stalk, and leaves are valued as forage and building material. In the USA, its mainly used for livestock feed and ethanol production, whereas, in China, it is popular for manufacturing traditional alcoholic beverages.
Sorghum’s remarkable ability to survive and produce yields under extreme climatic conditions compared to most other grain crops makes it an important 'failsafe' source of food, feed, fiber, and fuel in the global agroecosystem. Future projections regarding changing climate and its negative effect on yield traits, highlight the urgency to harness new genetic resources and the ability of breeding programs to develop the required adaptations promptly. Sorghum has numerous agro- ecological advantages over other crops like maize when it comes to temperate climates. But few of the biggest hurdles for sorghum adaptation to cooler climates are juvenile and reproductive cold stress.
The present study reported a genetic characterization of the diverse, previously uncharacterized S.bicolor collection of the Uganda National Genebank, representing different agro-ecological zones of the country. High-resolution genotyping using reduced representation sequencing was used to characterize the material and study population genetics. More than 3000 S. bicolor accessions were genotyped using a panel of around 20,000 genome-wide DArTseq SNP markers and co-analyzed with a global sorghum collection genotyped previously with the same panel of markers for genetic diversity analysis and studying different interesting traits. The results revealed the presence of extensive genetic and racial diversity in predominantly admixed accessions and a unique, genetically isolated group of accessions from the southwestern Ugandan highlands, a region which low temperatures which potentially harbors genes of interest for breeding of sorghum in Germany and other temperate climate zones.
A representative core set of the novel Ugandan sorghum germplasm was analyzed to study juvenile cold tolerance. Data was collected from multi-year field trials and controlled climate chamber experiments. Genome-wide association studies were used to identify genomic regions involved in adaptation to cooler climatic conditions that could be of interest for the expansion of sorghum
production into temperate latitudes. This thesis can be considered a case study to illustrate the potential of genebank genomics to screen valuable, underutilized germplasm collections to evaluate various biological and agro-economical traits and alleles.
While farmers can avoid early-stage cold stress by later sowing (albeit at the expense of maturity and yield potential), there is no escape strategy for reproductive stage cold stress. This trait was analysed in another broad diversity panel consisting of 330 inbred lines of different origin, types of use, and subspecies from multi-location field trials including tropical high-altitude and temperate environments. In this study, several significant marker-trait associations were identified. This was further combined with local LD analysis, previously curated QTL data, and synteny to potential candidate genes in rice and maize to narrow down to interesting marker-trait associations to specific genomic regions involved in cold stress response.
This thesis can be considered a basis for selecting accessions for genetic diversity preservation and management, utilization in breeding programs, and establishing genetic relationships with other existing germplasm collections. The results provide important new insights for adaptive crop breeding in the face of climate change and the expansion of sorghum production to different regions. This will facilitate sorghum from being a "plant of the future" to transforming into a real-life major agricultural alternative
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
